6ez0: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 6ez0 is ~~ON HOLD~~

==Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding==

== Structural highlights ==

<table><tr><td colspan='2'>[[6ez0]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EZ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EZ0 FirstGlance]. <br>

</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=U37:URIDINE+5-MONOTHIOPHOSPHATE'>U37</scene></td></tr>

<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2aht|2aht]]</td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ez0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ez0 OCA], [http://pdbe.org/6ez0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ez0 RCSB], [http://www.ebi.ac.uk/pdbsum/6ez0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ez0 ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Group II introns are large self-splicing ribozymes that require high amounts of monovalent and divalent metal ions for folding and catalysis under in vitro conditions. Domain 6 of these ribozymes contains a highly conserved adenosine whose 2'-OH acts as a nucleophile during self-cleavage via the branching pathway. We have previously suggested a divalent metal ion that binds to the major groove at the GU wobble pair above the branch-A in a minimal, but active branch domain construct (D6-27) from the yeast mitochondrial intron Sc.ai5gamma. Here we characterize metal ion binding to the phosphate oxygens at the branch site. In vitro transcription yielded a D6-27 construct where all R P oxygens of the uridine phosphate groups are replaced by sulfur (alpha-thio-D6-27). We determined its NMR structure, the second RNA-only structure containing thiophosphate groups. [(31)P] resonances were assigned and chemical shift changes monitored upon titration with Cd(2+). In addition, the two uridines flanking the branch-point, U19 and U21 were specifically thioated by chemical synthesis (thio-U19-D6-27 and thio-U19/U21-D6-27), enabling us to study Cd(2+) binding at the R P-, as well as the S P- position of the corresponding phosphate oxygens. Our studies reveal that both non-bridging phosphate oxygens of U19 are involved in metal ion coordination, whereas only the major groove phosphate oxygen of U21 is influenced. Together with NOE data of a hexaamminecobalt(III) titration, this suggests a single metal ion binding site at the GU wobble pair above the branch point in the major groove of D6 of this group II intron ribozyme.

~~Authors~~:

Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding.,Erat MC, Besic E, Oberhuber M, Johannsen S, Sigel RKO J Biol Inorg Chem. 2017 Dec 7. pii: 10.1007/s00775-017-1519-3. doi:, 10.1007/s00775-017-1519-3. PMID:29218637<ref>PMID:29218637</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased Structures~~]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Besic, E]]

[[Category: Erat, M C]]

[[Category: Johannsen, S]]

[[Category: Oberhuber, M]]

[[Category: Sigel, R K.O]]

[[Category: Rna]]

[[Category: Thiophosphate group ii intron branch-adenosine hairpin tetraloop]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6ez0 is ON HOLD
+==Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding==
+<StructureSection load='6ez0' size='340' side='right' caption='[[6ez0]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6ez0]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EZ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EZ0 FirstGlance]. <br>
+</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=U37:URIDINE+5-MONOTHIOPHOSPHATE'>U37</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2aht|2aht]]</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ez0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ez0 OCA], [http://pdbe.org/6ez0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ez0 RCSB], [http://www.ebi.ac.uk/pdbsum/6ez0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ez0 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Group II introns are large self-splicing ribozymes that require high amounts of monovalent and divalent metal ions for folding and catalysis under in vitro conditions. Domain 6 of these ribozymes contains a highly conserved adenosine whose 2'-OH acts as a nucleophile during self-cleavage via the branching pathway. We have previously suggested a divalent metal ion that binds to the major groove at the GU wobble pair above the branch-A in a minimal, but active branch domain construct (D6-27) from the yeast mitochondrial intron Sc.ai5gamma. Here we characterize metal ion binding to the phosphate oxygens at the branch site. In vitro transcription yielded a D6-27 construct where all R P oxygens of the uridine phosphate groups are replaced by sulfur (alpha-thio-D6-27). We determined its NMR structure, the second RNA-only structure containing thiophosphate groups. [(31)P] resonances were assigned and chemical shift changes monitored upon titration with Cd(2+). In addition, the two uridines flanking the branch-point, U19 and U21 were specifically thioated by chemical synthesis (thio-U19-D6-27 and thio-U19/U21-D6-27), enabling us to study Cd(2+) binding at the R P-, as well as the S P- position of the corresponding phosphate oxygens. Our studies reveal that both non-bridging phosphate oxygens of U19 are involved in metal ion coordination, whereas only the major groove phosphate oxygen of U21 is influenced. Together with NOE data of a hexaamminecobalt(III) titration, this suggests a single metal ion binding site at the GU wobble pair above the branch point in the major groove of D6 of this group II intron ribozyme.
-Authors:
+Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding.,Erat MC, Besic E, Oberhuber M, Johannsen S, Sigel RKO J Biol Inorg Chem. 2017 Dec 7. pii: 10.1007/s00775-017-1519-3. doi:, 10.1007/s00775-017-1519-3. PMID:29218637<ref>PMID:29218637</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6ez0" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Besic, E]]
+[[Category: Erat, M C]]
+[[Category: Johannsen, S]]
+[[Category: Oberhuber, M]]
+[[Category: Sigel, R K.O]]
+[[Category: Rna]]
+[[Category: Thiophosphate group ii intron branch-adenosine hairpin tetraloop]]